In my specific case I'm using a python env built using conda and not venv. When I ran make protogen it actually installed grpcio_tools=1.13.0 in my global env as pip3 was pointing to the global pip. Given that inside an environment pip points to the "correct" pip2 or pip3 depending on the python version of the environment I'd suggest to replace pip3 with pip.
If we're concerned about the python version I'd add a check that tests it before generating the python files.